An assay for evaluating hydrogen peroxide production by human neutrophils after stimulation using flow cytometry was developed and applied to patients with chronic granulomatous disease (CGD) and the X-linked obligate carriers. The flow cytometric dihydrorhodamine (DHR)-based assay for evaluation of oxidative burst is a sensitive method for evaluating phagocytes in patients with possible CGD. This assay also appears to be a good screen for the genotype of the disease. In addition, the method was optimized and is sensitive to 1 normal cell in <=10,000 abnormal cells making it an ideal assay for monitoring CGD patients after gene therapy, as well as for identifying normal cells after allogeneic granulocyte transfusion.